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Showing 1–21 of 21 results
Advanced filters: Author: Argyris Papantonis Clear advanced filters

  • By applying Hi-C to cells derived from the tumors of 24 GBM patients, the authors show pervasive structural variation in GBM chromosomal organization. How such patient-to-patient variation explains the characteristic gene expression patterns in each tumor is investigated.

    • Ting Xie
    • Adi Danieli-Mackay
    • Argyris Papantonis
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-16

  • High-resolution Micro-C is applied to characterize the effect of RNA polymerase II (RNAPII) loss on chromosome looping, finding that the formation of enhancer–promoter, but not promoter–promoter, loops are dependent on RNAPII binding to their anchors.

    • Shu Zhang
    • Nadine Übelmesser
    • Argyris Papantonis
    Research
    Nature Genetics
    Volume: 55, P: 832-840

  • Members of the CHD chromatin remodeler family are implicated in human pathologies, however CHD6 remained poorly studied. Here, the authors show that CHD6 binds to and regulates autophagy and stress response genes across cell types. They identify a clinical mutation that affects its ability to recruit cofactors, leading to impaired autophagy induction and DNA repair.

    • Yulia Kargapolova
    • Rizwan Rehimi
    • Argyris Papantonis
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-15

  • In this Review, Rippe and Papantonis describe advances in understanding the role of transcription compartments in gene regulation, specifically by collating and contrasting historical work on transcription factories with more recent work on transcriptional condensates.

    • Karsten Rippe
    • Argyris Papantonis
    Reviews
    Nature Reviews Genetics
    Volume: 26, P: 775-788

  • Seufert et al. analyse chromatin accessibility to identify sites that open simultaneously in response to TNF. They discover two distinct types of co-accessible regulatory module for controlling the induction of proinflammatory gene expression.

    • Isabelle Seufert
    • Irene Gerosa
    • Karsten Rippe
    Research
    Nature Cell Biology
    Volume: 28, P: 182-196

  • The early molecular events driving cancer initiation remain elusive, hampering prognostic accuracy. A comparative analysis of 3D genomics data from all stages of colon malignant transformation now reveals that altered connectivity of gene promoters with cognate enhancers is both predictive of and rate-limiting in neoplasia.

    • Adi Danieli-Mackay
    • Argyris Papantonis
    News & Views
    Nature Cancer
    Volume: 5, P: 1600-1601

  • Using single-molecule tracking of cohesin and CTCF during zebrafish embryogenesis, the molecular kinetics underlying chromatin architecture formation was revealed and gradual emergence of chromatin structure recapitulated by polymer simulations.

    • Jonas Coßmann
    • Pavel I. Kos
    • J. Christof M. Gebhardt
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18

  • Ubiquitination is a versatile modification system in eukaryotic cells. Here, the authors unveil that the ubiquitin ligase HUWE1 can modify drug-like small-molecule substrates, beyond proteins. This discovery may be harnessed to develop specific tool substrates or inhibitors of HECT-type ligases.

    • Barbara Orth
    • Pavel Pohl
    • Sonja Lorenz
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-19

  • Karpinska, Zhu and colleagues characterize the structure-function relationship of the genome during cellular differentiation and demonstrate a role for enhancer-promoter interactions in gene regulation that is independent of cooperative interactions in chromatin hubs.

    • Magdalena A. Karpinska
    • Yi Zhu
    • A. Marieke Oudelaar
    ResearchOpen Access
    Nature Structural & Molecular Biology
    Volume: 32, P: 1268-1281

  • The mechanisms of intratumoral subtype heterogeneity in pancreatic ductal adenocarcinoma (PDAC) remain unclear. Here, the authors analyse PDAC tumours and preclinical models using multi-omics and imaging; they demonstrate that AP1 dichotomy influences tumor plasticity, heterogeneity, and immune response, with potential therapeutic implications.

    • Lukas Klein
    • Mengyu Tu
    • Shiv K. Singh
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-19

  • Using CRISPR-guided editing, Liesenfelder et al. modify DNA methylation at epigenetic clock sites, which evokes genome-wide age-associated epigenetic modifications. Their findings suggest age-associated DNA methylation changes can be coherently modified within an epigenetic network.

    • Sven Liesenfelder
    • Mohamed H. Elsafi Mabrouk
    • Wolfgang Wagner
    ResearchOpen Access
    Nature Aging
    Volume: 5, P: 997-1009

  • The question of whether transcription factories containing RNA polymerases exist has been controversial, owing to the fact that they have not been isolated previously. Now, a method to carefully isolate these complexes and analyze their proteomes by mass spectrometry is described.

    • Svitlana Melnik
    • Binwei Deng
    • Peter R Cook
    Research
    Nature Methods
    Volume: 8, P: 963-968

  • Planarians are model systems for stem cells and regeneration. This study provides new genome assemblies of the model species S. mediterranea and 3 relatives and uses comparative genomics of planarians to reveal that synteny is not an evolutionary constraint in flatworm genome evolution.

    • Mario Ivanković
    • Jeremias N. Brand
    • Jochen C. Rink
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-21

  • During the repair of DNA breaks by homologous recombination, damaged DNA seeks out intact, similar in sequence segments to use as a template. In this issue, Piazza, Bordelet and colleagues describe three-dimensional chromosome architecture remodelling during homologous recombination and show that cohesin restricts homology search in cis, independently of sister chromatid cohesion.

    • Argyris Papantonis
    • Vassilis Roukos
    News & Views
    Nature Cell Biology
    Volume: 23, P: 1112-1114

  • Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.

    • Julia Franzen
    • Theodoros Georgomanolis
    • Wolfgang Wagner
    ResearchOpen Access
    Communications Biology
    Volume: 4, P: 1-12